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Merge "Merge branch release-4-6 into release-5-0" into release-5-0
2014-05-09
R
olan
d
Schulz
Merge "Merge branch rele
a
se-4-6 i
n
to r
e
l
e
a
s
e-5-0"
into
.
.
.
commit
|
commitdiff
|
tree
2014-05-09
Ro
l
and S
c
hulz
Fix OpenMP scope
err
o
r
commit
|
commitdiff
|
tree
2014-04-29
Berk Hess
Remov
e
d trunca
t
ion of n
r
df in v-resca
l
e t
h
erm
o
s
tat
commit
|
commitdiff
|
tree
2014-04-24
Magnus Lu
n
d
borg
M
o
re
efficie
n
t
T
NG s
e
lection
group
c
reation
commit
|
commitdiff
|
tree
2014-04-23
Berk Hess
Fixed n
b
nxn F
E
list allocation issue
commit
|
commitdiff
|
tree
2014-04-21
M
i
ch
a
el S
h
i
rts
Issue
w
arnings for potential
s
wi
t
ch w/o defining switch
.
.
.
commit
|
commitdiff
|
tree
2014-04-16
Magnus Lundbo
r
g
Fixed bug invertin
g
c
o
mpress
i
on precision
.
commit
|
commitdiff
|
tree
2014-04-16
Mark Ab
r
aham
Fix and simplify versi
o
n matching for
running tests
commit
|
commitdiff
|
tree
2014-04-07
M
a
rk Abraham
Fix invalid derefere
n
ce
i
n
g_tune_
p
m
e
commit
|
commitdiff
|
tree
2014-04-07
E
rik Lindahl
Make sure water optimiz
a
t
i
o
n is dis
a
bled
for esoter
i
c
.
.
.
commit
|
commitdiff
|
tree
2014-04-07
Teemu Murt
o
la
D
o
x
yge
n
documentation for
version
.
h
commit
|
commitdiff
|
tree
2014-04-03
Mark Abraham
Move st
r
ing-par
s
ing code to where it can
b
e
r
eus
e
d
commit
|
commitdiff
|
tree
2014-04-02
Roland Schulz
Add doc
f
or s
p
e
c
.
values of
G
MX_
M
AXBACKUP
commit
|
commitdiff
|
tree
2014-04-02
David
van de
r
Spoe
l
R
e
moved possibility of compiling with GS
L
.
commit
|
commitdiff
|
tree
2014-04-02
Teemu M
u
r
t
ol
a
Move string2
.
* to utility/cstringutil
.
*
commit
|
commitdiff
|
tree
2014-04-02
Mark Ab
r
ah
a
m
Fixes for g_
t
u
ne
_
p
me
f
or 5
.
0
commit
|
commitdiff
|
tree
2014-04-02
Ma
r
k
Ab
r
aham
Fix bu
g
accumulati
n
g
nrank_pp_intranode on PME r
a
nks
commit
|
commitdiff
|
tree
2014-04-02
Ber
k
H
e
ss
Adde
d
LJ-PME
and
LJ Po
t
-
s
wi
t
ch
t
o
P
ME load estimate
commit
|
commitdiff
|
tree
2014-04-02
Mark Ab
r
aham
R
e-use
gmx_gre
a
test_common_divis
o
r()
commit
|
commitdiff
|
tree
2014-04-01
Teemu Murtola
Move s
m
alloc
.
h to
utility/
commit
|
commitdiff
|
tree
2014-03-31
David van der Spoel
Fixed compilation issue
in f
g
rid
.
c
pp due to int/enum
commit
|
commitdiff
|
tree
2014-03-31
M
a
rk Abraham
Remove
q
uote
commit
|
commitdiff
|
tree
2014-03-31
Rossen Ap
o
stolov
Added CMa
k
e support for Ex
t
rae
.
commit
|
commitdiff
|
tree
2014-03-31
Tee
m
u Mur
t
ol
a
Clean u
p
s
m
a
l
loc
.
h
commit
|
commitdiff
|
tree
2014-03-31
Carsten Kutz
n
er
Fix documentatio
n
o
f
swap/enums
.
h
commit
|
commitdiff
|
tree
2014-03-31
Roland Schulz
Disable shared libraries
b
y d
e
fault for mdrun
-
only
commit
|
commitdiff
|
tree
2014-03-31
Teemu Murto
l
a
Remove de
p
endency on
c
ommand
l
ine/ fr
o
m oenv
.
cpp
commit
|
commitdiff
|
tree
2014-03-29
Christia
n
W
e
nnbe
r
g
Free-energy
s
upport for L
J
-PME
commit
|
commitdiff
|
tree
2014-03-29
Teemu Murtola
O
ptim
i
z
e int
e
rmodule dependencies
commit
|
commitdiff
|
tree
2014-03-29
T
e
e
m
u Murtola
Improve v
e
rsion information handl
i
ng
commit
|
commitdiff
|
tree
2014-03-29
Teem
u
Murtol
a
Be
t
ter i
n
cl
u
de de
p
endency graph genera
t
or
commit
|
commitdiff
|
tree
2014-03-28
Carsten Kutzner
Fix documentation issues f
o
r
interacti
v
e M
D
modu
l
e
.
commit
|
commitdiff
|
tree
2014-03-28
Christian W
e
nnberg
N
e
w V
D
W k
e
rnel
flav
o
ur for
L
J-P
M
E and
u
pdat
e
d group
.
.
.
commit
|
commitdiff
|
tree
2014-03-26
Daniel Landau
Add Cray compi
l
er
support
commit
|
commitdiff
|
tree
2014-03-26
Carsten K
u
tzner
Doc
u
men
t
ation house
-
ke
e
p
ing in file
s
wapcoords
.
c
commit
|
commitdiff
|
tree
2014-03-26
Mart
i
n Hoe
f
ling
Interactive Molecul
a
r Dynamic
s
(IMD)
commit
|
commitdiff
|
tree
2014-03-23
Mark Abr
a
h
am
Keep CMak
e
quiet about
n
on-
d
etect
i
o
n of
o
ptional st
u
ff
commit
|
commitdiff
|
tree
2014-03-23
Ber
k
Hes
s
Fixed bug
i
n p
a
rallel
v/f constra
i
ning
commit
|
commitdiff
|
tree
2014-03-23
Ber
k
Hess
CUDA cut-of
f
k
e
r
n
els now
s
hif
t
ex
c
lusion ener
g
ies
commit
|
commitdiff
|
tree
2014-03-23
M
ark Abraham
Fix print_da
t
e_a
n
d_time
commit
|
commitdiff
|
tree
2014-03-18
R
o
land Schulz
Fix dependencies on config
.
h
for typedefs
.
h
commit
|
commitdiff
|
tree
2014-03-18
Christia
n
Wennberg
Bugfix in LJ-PME without electrost
a
t
ics
commit
|
commitdiff
|
tree
2014-03-18
Mark Abraham
Removed more stuff related to gmx
.
f
f and gmx2
.
ff
commit
|
commitdiff
|
tree
2014-03-18
T
e
emu Murtola
Remove interactive help fro
m
core
s
ele
c
tion
parser
commit
|
commitdiff
|
tree
2014-03-18
T
e
emu Murto
l
a
Im
p
rove
interac
t
ive selecti
o
n inpu
t
commit
|
commitdiff
|
tree
2014-03-17
R
o
ssen Apostolov
Clea
n
ed up endif/else-s in CMakeLists
.
t
x
t
a
nd *
.
c
m
a
k
e
.
.
.
commit
|
commitdiff
|
tree
2014-03-17
M
a
rk Abraham
M
e
rge "Me
r
ge branch
rel
e
a
se-4
-
6
"
commit
|
commitdiff
|
tree
2014-03-17
Ma
r
k Abrah
a
m
Fix perturbation
to Verlet sc
h
eme when not pertu
r
bing
commit
|
commitdiff
|
tree
2014-03-14
C
a
r
s
t
e
n K
u
t
zner
Avoid cros
s
produ
c
t
with zero vecto
r
i
n rotational
.
.
.
commit
|
commitdiff
|
tree
2014-03-11
Mar
k
Ab
r
aham
Fix
M
KL linkin
g
commit
|
commitdiff
|
tree
2014-03-11
Mark Abraham
Av
o
id
arra
y
-bounds warnings with g
c
c
4
.
8
.
2
commit
|
commitdiff
|
tree
2014-03-11
Roland Schulz
S
i
mplify gmxTestLibXm
l
2
commit
|
commitdiff
|
tree
2014-03-11
Berk
H
ess
PME load bala
n
cing no
w
works
w
i
th LJ
-
PME
commit
|
commitdiff
|
tree
2014-03-11
Te
e
mu Murto
l
a
Fi
x
misc
.
D
o
xygen
i
ssue
s
commit
|
commitdiff
|
tree
2014-03-11
Rol
a
nd Sc
h
ul
z
F
i
x Check
C
XXCompile
r
Flag
commit
|
commitdiff
|
tree
2014-03-11
Szilárd Páll
B
ump required CUDA version to 4
.
0
commit
|
commitdiff
|
tree
2014-03-11
R
oland Schulz
Replace inlin
e
with gmx_inline
commit
|
commitdiff
|
tree
2014-03-10
Mark Abrah
a
m
Fix dependency on swapcoord
s
e
nu
m
s
commit
|
commitdiff
|
tree
2014-03-06
R
o
l
and Schulz
Remove
K
ER
N
EL_WIDTH
commit
|
commitdiff
|
tree
2014-03-06
Rossen Aposto
l
ov
Removed t
h
e depre
c
a
ted gmx
.
ff
a
nd gmx2
.
f
f
.
commit
|
commitdiff
|
tree
2014-03-06
Rolan
d
Schulz
U
se gmx_int64_t for gmx_
o
ff_t
commit
|
commitdiff
|
tree
2014-03-06
Berk H
e
ss
Fixed
e
xit with FEP with PME nod
e
s w
i
thout L
J
-
P
ME
commit
|
commitdiff
|
tree
2014-03-06
ngoga
Martini CG - Combined ang
l
e
-
t
orsion pot
e
ntials
commit
|
commitdiff
|
tree
2014-03-06
David
v
an der Sp
o
el
Six new quotes from
c
lassic lit
e
r
ature
.
commit
|
commitdiff
|
tree
2014-03-05
Ro
l
and Schulz
Remove de
p
endency on TNG in
t
r
xio
.
h
commit
|
commitdiff
|
tree
2014-03-05
Rola
n
d S
c
hulz
Re
p
ort MIC S
I
M
D corre
c
tly
commit
|
commitdiff
|
tree
2014-03-05
Mark Abraham
M
erge "Merg
e
relea
s
e-4-6 into master
"
commit
|
commitdiff
|
tree
2014-03-05
Berk
Hess
Buffer estimat
e
now wor
k
s with rvd-switch=0
commit
|
commitdiff
|
tree
2014-03-05
Rola
n
d Schulz
Chec
k
zlib
c
an
a
ctually
be linke
d
commit
|
commitdiff
|
tree
2014-03-05
Rol
a
nd Schulz
Avoid
segfaul
t
whe
n
co
m
par
i
ng
tpr
commit
|
commitdiff
|
tree
2014-03-04
Mark Abr
a
ham
Add enum and d
o
c
s for usi
n
g tp
x
_ver
s
ion
commit
|
commitdiff
|
tree
2014-03-02
Teemu Murtola
Fix incorrect grid ce
l
l size
i
n
g_
s
as -nopbc
commit
|
commitdiff
|
tree
2014-03-01
Teemu Murtola
Move default
l
i
bra
r
y path
s
earch to program context
commit
|
commitdiff
|
tree
2014-03-01
Mark Abr
a
h
a
m
Add fatal error
for
A
nder
s
en+c
o
nstrai
n
ts+D
D
commit
|
commitdiff
|
tree
2014-03-01
C
h
ristoph Jun
g
hans
switch ld_seed from int to
g
mx_int64_t
commit
|
commitdiff
|
tree
2014-03-01
S
z
ilard Pall
Added C
U
DA LJ-P
M
E nbnxn ker
n
els
commit
|
commitdiff
|
tree
2014-02-27
T
e
emu Murtola
Improve support for data sets in
C
++ tools
commit
|
commitdiff
|
tree
2014-02-27
Szi
l
ard Pall
CUDA kernels for switched LJ
commit
|
commitdiff
|
tree
2014-02-27
Teemu Mu
r
t
ola
I
m
prove floating point comparisons in unit tests
commit
|
commitdiff
|
tree
2014-02-26
Berk H
e
ss
Free-energy
n
o
w
works with the
Verlet scheme
commit
|
commitdiff
|
tree
2014-02-26
Al
e
xey S
h
v
e
tsov
Fix -Wmaybe-unin
i
tialized warn
i
ngs i
n
some fil
e
s
commit
|
commitdiff
|
tree
2014-02-26
Teemu Murto
l
a
Misc
.
Do
x
ygen
bui
l
d syst
e
m improvemen
t
s
commit
|
commitdiff
|
tree
2014-02-26
Erik L
i
n
d
ahl
Ad
d
ed message to warn tha
t
group
k
e
rnels are deprecated
.
commit
|
commitdiff
|
tree
2014-02-26
M
i
c
hael Shirts
Upd
a
ting
a
nd impro
v
ing Ander
s
en thermo
s
t
a
t docu
m
enta
t
ion
commit
|
commitdiff
|
tree
2014-02-26
Rola
n
d Sch
u
lz
ICC aliasing optimization flags
commit
|
commitdiff
|
tree
2014-02-26
R
o
land Schulz
Replace
a
ll md
r
un r
n
g
s
wit
h
cycle bas
e
d rng
commit
|
commitdiff
|
tree
2014-02-26
Ma
r
k Abraham
A
d
d Threa
d
Sanitizer b
u
il
d
type
commit
|
commitdiff
|
tree
2014-02-25
Berk Hess
Fixes s
e
perate P
M
E nodes
without
LJ-
P
ME
commit
|
commitdiff
|
tree
2014-02-24
Berk Hess
F
ixed bug with
LJ pot-
s
witch in 4xN k
e
rnels
commit
|
commitdiff
|
tree
2014-02-24
Mark Abraham
Permit
wa
r
ning-fr
e
e use of Andersen thermostat
commit
|
commitdiff
|
tree
2014-02-24
Mark Abraham
Su
p
pr
e
s
s
icc warning for Boost 1
.
55 use of #pragma
.
.
.
commit
|
commitdiff
|
tree
2014-02-23
Ros
s
en Apostolov
Removed deprecat
e
d Encad FF
.
commit
|
commitdiff
|
tree
2014-02-21
Roland Sc
h
ulz
Fix load_lj_pa
i
r_params2 fo
r
MIC
commit
|
commitdiff
|
tree
2014-02-21
Roland Sc
h
u
l
z
Updated Boost
to
l
ate
s
t 1
.
55
.
0
commit
|
commitdiff
|
tree
2014-02-21
Rola
n
d Schulz
M
e
rge
"Mer
g
e release-4-6 i
n
to master"
commit
|
commitdiff
|
tree
2014-02-20
Mar
k
Abraham
Remo
v
e
p
article decompo
s
i
ti
o
n
commit
|
commitdiff
|
tree
2014-02-20
Christoph
J
ung
h
ans
added gmx_is_{sin
g
le,do
u
b
l
e}_precisi
o
n
commit
|
commitdiff
|
tree
2014-02-20
Roland Schulz
Fix aligned s
t
o
re to unaligned memory
commit
|
commitdiff
|
tree
2014-02-20
Ma
r
k
A
braham
avoid
m
drun cra
s
h when rdtscp is not s
u
pp
o
rted
commit
|
commitdiff
|
tree
2014-02-20
M
a
rk Abrah
a
m
A
dd inte
g
ration
t
ests for repli
c
a exchange
commit
|
commitdiff
|
tree
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